Studies indicate that significant inter-individual variation exists at the amino acid sequence level of BER proteins and in BER capacity among individuals within the population. We have initiated efforts to delineate the impact of amino acid variants found in BER proteins and to develop assays to determine the extent of inter-individual variation in BER effectiveness. Our recent work has focused on variants in the major human abasic endonuclease (APE1), and found that except for the endometrial cancer-associated variant R237C, the polymorphic variants Q51H, I64V and D148E, the rare population variants G241R, P311S and A317V, and the tumor-associated variant P112L exhibit normal thermodynamic stability of protein folding; abasic endonuclease, 3'-5' exonuclease and REF-1 activities; coordination during the early steps of base excision repair; and intracellular distribution when expressed exogenously in HeLa cells. The R237C mutant displayed reduced AP-DNA complex stability, 3'-5' exonuclease activity and 3'-damage processing. Re-sequencing of the exonic regions of APE1 uncovered no novel amino acid substitutions in the 60 cancer cell lines of the NCI-60 panel, or in HeLa or T98G cancer cell lines; only the common D148E and Q51H variants were observed. Our results indicate that APE1 missense mutations are seemingly rare and that the cancer-associated R237C variant may represent a reduced-function susceptibility allele. In addition, using established biochemical assays, our initial results indicate that for AP site incision, an 1.9-fold inter-individual variation in repair capacity exists among the twenty-three individuals examined thus far. For gap-filling and nick ligation, an 1.3-fold and 3.4-fold inter-individual variation was observed, respectively. We are currently designing a series of more sophisticated high-throughput assays to more thoroughly evaluate the relationship of BER capacity with disease susceptibility and premature aging phenotypes. Current strategies to eradicate cancer cells commonly employ agents that generate DNA lesions that induce cell death by blocking replication of rapidly dividing cells. Thus, a goal has been to regulate strategically the repair capacity of cancer and/or normal cells to improve the efficacy of specific therapeutic paradigms. In particular, inhibiting the DNA repair capacity of cancerous cells has been an area of growing interest. Our results indicate that APE1, and BER more generally, is a reasonable target for inactivation in anti-cancer treatment paradigms involving select alkylating drugs (e.g., temozolomide) and antimetabolites (e.g., 5-fluorouracil). Moreover, we have found recently that BER, and APE1 in particular, are promising targets for treating cancers with a deficiency in homologous recombination via an approach that involves synergistic (or synthetic) lethality, and that the flap endonuclease, FEN1, is a promising biomarker in breast and ovarian epithelial cancer. Finally, we have developed a panel of complementary and improved miniaturized high-throughput screening and profiling assays, which will have a broad appeal to other research investigators, particularly those in the field of DNA repair. These assays have permitted the identification of novel, small molecule APE1-targeted bioactive inhibitors, which we are aiming to optimize with the long term goal of creating high affinity, selective inhibitors with therapeutic value. The establishment of small molecule probes will provide a platform for more extensive investigations on the therapeutic benefits of regulating cellular DNA repair capacity.